Workflow: Merge, annotate, and generate a TSV for SVs
Fetched 2023-01-15 00:33:04 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| sv_vcfs | File[] | ||
| snps_vcf | File (Optional) | ||
| same_type | Boolean | ||
| cohort_name | String (Optional) | ||
| same_strand | Boolean | ||
| genome_build | String | ||
| blocklist_bedpe | File (Optional) | ||
| minimum_sv_size | Integer | ||
| minimum_sv_calls | Integer | ||
| estimate_sv_distance | Boolean | ||
| max_distance_to_merge | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bcftools_merge_sv_vcfs |
../tools/bcftools_merge.cwl
(CommandLineTool)
|
||
| survivor_merge_sv_vcfs |
../tools/survivor.cwl
(CommandLineTool)
|
Run SURVIVOR to merge SV calls | |
| bcftools_annotsv_filter |
../tools/annotsv_filter.cwl
(CommandLineTool)
|
filter AnnotSV tsv output generated from a bcftools merged vcf | |
| filter_blocklist_bcftools |
../tools/filter_sv_vcf_blocklist_bedpe.cwl
(CommandLineTool)
|
||
| filter_blocklist_survivor |
../tools/filter_sv_vcf_blocklist_bedpe.cwl
(CommandLineTool)
|
||
| bcftools_annotate_variants |
../tools/annotsv.cwl
(CommandLineTool)
|
||
| survivor_annotate_variants |
../tools/annotsv.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bcftools_merged_sv_vcf | File | ||
| survivor_merged_sv_vcf | File | ||
| bcftools_merged_annotated_tsv | File | ||
| survivor_merged_annotated_tsv | File | ||
| bcftools_merged_filtered_annotated_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/3a287b7cb6162cdea79865235d224fea45963d87/definitions/subworkflows/merge_svs.cwl
